title: Hypothetical in silico model of the early-stage intermediate in protein folding.
abstract: This paper presents a method for determining the structure of the early stage (ES) intermediate in the multistage protein folding process. ES structure is modeled on the basis of a limited conformational subspace of the Ramachandran plot. The model distinguishes seven structural motifs corresponding to seven local probability maxima within the limited conformational subspace. Three of these are assigned to well-defined secondary structures, while the remaining four are found to represent various types of random coils. The presented heuristic approach also provides insight into the reasons behind incorrect predictions occurring when the folding process depends on external factors (e.g., ligands, ions or other proteins) rather than on the characteristics of the backbone itself. The accuracy of the presented method is estimated at around 48 %.
authors.affiliation: Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Lazarza 16, 31-530, Krakow, Poland.
authors.forename: Barbara
authors.initials: B
authors.lastname: Kalinowska
authors.forename: Paweł
authors.initials: P
authors.lastname: Alejster
authors.forename: Kinga
authors.initials: K
authors.lastname: Sałapa
authors.forename: Zbigniew
authors.initials: Z
authors.lastname: Baster
authors.forename: Irena
authors.initials: I
authors.lastname: Roterman
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins